diff --git a/master_changes.md b/master_changes.md
index 836232e95c4..285829af845 100644
--- a/master_changes.md
+++ b/master_changes.md
@@ -132,6 +132,8 @@ users)
   * [BUG] Fix `opam admin check` in the presence of the `with-dev-setup` variable [#6331 @kit-ty-kate - fix #6329]
   * ✘ The `-i`/`--ignore-test-doc` argument has been removed from `opam admin check` [#6335 @kit-ty-kate]
   * ✘ `opam admin check` now sets `with-test` and `with-doc` to `false` instead of `true` [#6335 @kit-ty-kate]
+  * Enforce repository root check for all command [#6385 @rjbou]
+  * Add an upgrade advice is the repository is 1.2 version, for all command except upgrade [#6385 @rjbou]
 
 ## Opam installer
 
@@ -175,6 +177,7 @@ users)
   * Add a test showing the behaviour of `opam upgrade` with packages flagged with `avoid-version`/`deprecated` [#6273 @kit-ty-kate]
   * Add a test showing the behaviour when a pin depend is unpinned [#6380 @rjbou]
   * Add a test to ensure `opam upgrade <pkg>` will not upgrade unrelated things [#6373 @kit-ty-kate]
+  * Add a test in admin to test repository version upgrade advice [#6385 @rjbou]
 
 ### Engine
 
diff --git a/src/client/opamAdminCommand.ml b/src/client/opamAdminCommand.ml
index e564dd95d1a..705dad6e9d7 100644
--- a/src/client/opamAdminCommand.ml
+++ b/src/client/opamAdminCommand.ml
@@ -16,13 +16,33 @@ open Cmdliner
 
 type command = unit Cmdliner.Term.t * Cmdliner.Cmd.info
 
-let checked_repo_root () =
+let repo_version_lt repo_root v =
+  let v' =
+    let open OpamStd.Option.Op in
+    (OpamFile.Repo.read_opt
+       (OpamRepositoryPath.repo repo_root)
+     >>= OpamFile.Repo.opam_version)
+    +! (OpamVersion.of_string "1.2")
+  in
+  if OpamVersion.compare v v' > 0 then Some v' else None
+
+let checked_repo_root ?(check=true)() =
   let repo_root = OpamFilename.cwd () in
   if not (OpamFilename.exists_dir (OpamRepositoryPath.packages_dir repo_root))
   then
     OpamConsole.error_and_exit `Bad_arguments
       "No repository found in current directory.\n\
        Please make sure there is a \"packages%s\" directory" OpamArg.dir_sep;
+  (if check then
+     let default_current = "2.0" in
+     match repo_version_lt repo_root
+             (OpamVersion.of_string default_current) with
+     | Some v ->
+       OpamConsole.warning
+         "The repository is at version %s, \
+          please consider upgrading to %s with 'opam admin upgrade'"
+         (OpamVersion.to_string v) default_current
+     | None -> ());
   repo_root
 
 let global_options cli =
@@ -76,7 +96,7 @@ let index_command cli =
   in
   let cmd global_options urls_txt () =
     OpamArg.apply_global_options cli global_options;
-    let repo_root = checked_repo_root ()  in
+    let repo_root = checked_repo_root () in
     let repo_file = OpamRepositoryPath.repo repo_root in
     let repo_def =
       match OpamFile.Repo.read_opt repo_file with
@@ -646,10 +666,11 @@ let upgrade_command cli =
   in
   let cmd global_options clear_cache create_mirror () =
     OpamArg.apply_global_options cli global_options;
+    let repo_root = checked_repo_root ~check:false () in
     if clear_cache then OpamAdminRepoUpgrade.clear_cache ()
     else match create_mirror with
       | None ->
-        OpamAdminRepoUpgrade.do_upgrade (OpamFilename.cwd ());
+        OpamAdminRepoUpgrade.do_upgrade repo_root;
         if OpamFilename.exists (OpamFilename.of_string "index.tar.gz") ||
            OpamFilename.exists (OpamFilename.of_string "urls.txt")
         then
@@ -657,7 +678,7 @@ let upgrade_command cli =
             "Indexes need updating: you should now run:\n\
              \n\
             \  opam admin index"
-      | Some m -> OpamAdminRepoUpgrade.do_upgrade_mirror (OpamFilename.cwd ()) m
+      | Some m -> OpamAdminRepoUpgrade.do_upgrade_mirror repo_root m
   in
   OpamArg.mk_command  ~cli OpamArg.cli_original command ~doc ~man
     Term.(const cmd $ global_options cli $
@@ -702,7 +723,7 @@ let lint_command cli =
   in
   let cmd global_options short list incl excl ign warn_error () =
     OpamArg.apply_global_options cli global_options;
-    let repo_root = OpamFilename.cwd () in
+    let repo_root = checked_repo_root () in
     if not (OpamFilename.exists_dir OpamFilename.Op.(repo_root / "packages"))
     then
         OpamConsole.error_and_exit `Bad_arguments
@@ -1014,6 +1035,7 @@ let list_command cli =
       global_options package_selection disjunction state_selection
       package_listing env packages () =
     OpamArg.apply_global_options cli global_options;
+    let repo_root = checked_repo_root () in
     let format =
       let force_all_versions =
         match packages with
@@ -1040,7 +1062,7 @@ let list_command cli =
               List.map (fun x -> Atom x) package_selection);
       ]
     in
-    let st = get_virtual_switch_state (OpamFilename.cwd ()) env in
+    let st = get_virtual_switch_state repo_root env in
     if not format.OpamListCommand.short && filter <> OpamFormula.Empty then
       OpamConsole.msg "# Packages matching: %s\n"
         (OpamListCommand.string_of_formula filter);
@@ -1081,7 +1103,7 @@ let filter_command cli =
       global_options package_selection disjunction state_selection env
       remove dryrun packages () =
     OpamArg.apply_global_options cli global_options;
-    let repo_root = OpamFilename.cwd () in
+    let repo_root = checked_repo_root () in
     let pattern_selector = OpamListCommand.pattern_selector packages in
     let join =
       if disjunction then OpamFormula.ors else OpamFormula.ands
diff --git a/tests/reftests/admin-cache.test b/tests/reftests/admin-cache.test
index af344519b90..5c02cb49ce0 100644
--- a/tests/reftests/admin-cache.test
+++ b/tests/reftests/admin-cache.test
@@ -1,10 +1,8 @@
 N0REP0
-### mv REPO OPER
-### opam repository set-url default OPER/ --set-default
-[default] Initialised
 ### : create repo
+### rm -rf REPO
 ### <repo>
-opam-version: "1.2"
+opam-version: "2.0"
 ### <packages/ipsum/ipsum.1/opam>
 opam-version: "2.0"
 ### <packages/dolor/dolor.1/opam>
@@ -252,7 +250,7 @@ amet : md5 : exists, link to sha512
 amet : sha256 : exists, link to sha512
 amet : sha512 : exists
 ### ::::::::::::::::::::::::::::::::::::
-### :IV: add a other hashes afterwards :
+### :IV: add another hashes afterwards :
 ### ::::::::::::::::::::::::::::::::::::
 ### : ipsum : only md5 then adding sha512
 ### : dolor : md5 & sha256 then adding sha512
diff --git a/tests/reftests/admin.test b/tests/reftests/admin.test
index 415f3f01db8..80dcdd0c6c4 100644
--- a/tests/reftests/admin.test
+++ b/tests/reftests/admin.test
@@ -766,3 +766,23 @@ no-extra.1
 no-extra.2
 ### opam admin list --short --all-versions --latests-only
 no-extra.2
+### ::: Test opam repo version warning
+### rm -rf packages
+### <packages/dummy/dummy.1/opam>
+opam-version: "2.0"
+### : repo 1.2
+### <repo>
+opam-version: "1.2"
+### opam admin list --short
+[WARNING] The repository is at version 1.2, please consider upgrading to 2.0 with 'opam admin upgrade'
+dummy
+### : missing repo, assuming 1.2
+### rm repo
+### opam admin list --short
+[WARNING] The repository is at version 1.2, please consider upgrading to 2.0 with 'opam admin upgrade'
+dummy
+### : repo 2.0
+### <repo>
+opam-version: "2.0"
+### opam admin list --short
+dummy